Hi Mike,
Finally managed to get a copy of FC yesterday evening; nice pics and write-up.
I'm not proclaiming to be an expert, but I've had something similar to this happen to me. In the end, it was a coilpack that was intermitantly faulty, and didn't completely run smooth again unitl all four packs were replaced. Bear in mind that when a cylinder has below-par voltage, it may cause a sluggish motion and this maybe the cause of the knock in the cylinder; engines tend to knock when they run rough. Get a voltmeter and clip it to each each wire feed individually, it should read roughly 14 volts. Any less at any point, it could be a dirty connection within the loom, or at the point of the coil pack.
Cheekily, I called out the AA when mine started to play up, and this is what he did, before my mechanic repeating the same process.
No expert in any shape or form mate, but this was my experience. Thought it might
help. Keep the faith. It'll be something very minor and soon it'll run sweet as a nut again.
Loving the Green
James.